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Molecular Modeling Database

Abbreviation:MMDB

General Information

The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more.

Homepage https://www.ncbi.nlm.nih.gov/structure

Countries that developed this resource United States

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: MMDB; Molecular Modeling Database; DOI: https://doi.org/10.25504/FAIRsharing.zqzvyc; Last edited: April 26, 2021, 3:42 p.m.; Last accessed: Sep 16 2021 10:03 p.m.

This record is maintained by marchlerbauer ORCID

Record updated: April 26, 2021, 3:41 p.m. by marchlerbauer.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.zqzvyc' by 'marchlerbauer' at 15:41, 26 Apr 2021 (approved):

	'tools' has been modified:
		Before:
			Entrez structure search||http://www.ncbi.nlm.nih.gov/structure
			Cn3D structure viewer|4.3.1|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
			BLAST||http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb
			VAST Search for Similar Structures||http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
			VAST+ similar structure assemblies||http://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi
		After:
			Entrez structure search||http://www.ncbi.nlm.nih.gov/structure
			Cn3D structure viewer|4.3.1|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
			BLAST||http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb
			VAST Search for Similar Structures||http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
			VAST+ similar structure assemblies||http://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi
			iCn3D - WebGL-based 3D structure viewer|2.24.7|https://www.ncbi.nlm.nih.gov/Structure/icn3d/
		Added:
			iCn3D - WebGL-based 3D structure viewer|2.24.7|https://www.ncbi.nlm.nih.gov/Structure/icn3d/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.zqzvyc' by 'The FAIRsharing Team' at 16:57, 20 Apr 2021 (approved):

	'name' has been modified:
		Before: Molecular Modeling Database (MMDB)
		After: Molecular Modeling Database

	'onto_domains' has been modified:
		Before:
			deoxyribonucleic acid
			modeling and simulation objective
			molecular interaction
			protein
			small molecule
			structure
		After:
			Structure
			deoxyribonucleic acid
			modeling and simulation objective
			molecular interaction
			protein
			small molecule
			structure
		Added:
			Structure
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.zqzvyc' by 'The FAIRsharing Team' at 13:47, 12 Jan 2018 (approved):

	'homepage' has been modified:
		Before: http://www.ncbi.nlm.nih.gov/Structure/
		After: https://www.ncbi.nlm.nih.gov/structure

Edits to 'https://fairsharing.org/FAIRsharing.zqzvyc' by 'The FAIRsharing Team' at 14:14, 16 Sep 2016 (approved):

	'homepage' has been modified:
		Before: http://www.ncbi.nlm.nih.gov/structure
		After: http://www.ncbi.nlm.nih.gov/Structure/

Support

General

help	http://www.ncbi.nlm.nih.gov/Structure/cd ...

Additional Information

Contact

Thomas Madej

Tools

Entrez structure search	http://www.ncbi.nlm.nih.gov/structure
Cn3D structure viewer	http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml	4.3.1
BLAST	http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&B ...
VAST Search for Similar Structures	http://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html
VAST+ similar structure assemblies	http://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi
iCn3D - WebGL-based 3D structure viewer	https://www.ncbi.nlm.nih.gov/Structure/icn3d/	2.24.7

Access / Retrieve Data

Conditions of Use

Applies to: Data use

NCBI Website and Data Usage Policies and Disclaimers

Data Access

Download

ftp://ftp.ncbi.nih.gov/mmdb/

Publications

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Wang Y., Addess KJ., Chen J., Geer LY., He J., He S., Lu S., Madej T., Marchler-Bauer A., Thiessen PA., Zhang N., Bryant SH.,
Nucleic Acids Res. 2007

View Paper (PubMed)

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Madej T,Lanczycki CJ,Zhang D,Thiessen PA,Geer RC,Marchler-Bauer A,Bryant SH
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

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Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by marchlerbauer ORCID

Maintains

National Center for Biotechnology Information (NCBI), Rockville, MD, USA (Government body)

Molecular Modeling Database

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